Extant eukaryotic cells have a dynamic traffic network that consists of diverse membrane-bound organelles exchanging matter via vesicles. This endomembrane system arose and diversified during a period characterized by massive expansions of gene families involved in trafficking after the acquisition of a mitochondrial endosymbiont by a prokaryotic host cell >1.8 billion years ago. Here we investigate the mechanistic link between gene duplication and the emergence of new nonendosymbiotic organelles, using a minimal biophysical model of traffic. Our model incorporates membrane-bound compartments, coat proteins and adaptors that drive vesicles to bud and segregate cargo from source compartments, and SNARE proteins and associated factors that cause vesicles to fuse into specific destination compartments. In simulations, arbitrary numbers of compartments with heterogeneous initial compositions segregate into a few compositionally distinct subsets that we term organelles. The global structure of the traffic system (i.e., the number, composition, and connectivity of organelles) is determined completely by local molecular interactions. On evolutionary timescales, duplication of the budding and fusion machinery followed by loss of cross-interactions leads to the emergence of new organelles, with increased molecular specificity being necessary to maintain larger organellar repertoires. These results clarify potential modes of early eukaryotic evolution as well as more recent eukaryotic diversification.

Communities of interdependent microbes, found in diverse natural contexts, have recently attracted the attention of bioengineers. Such consortia have potential applications in biosynthesis, with metabolic tasks distributed over several phenotypes, and in live-cell microbicide therapies where phenotypic diversity might aid in immune evasion. Here we investigate one route to generate synthetic microbial consortia and to regulate their phenotypic diversity, through programmed genetic interconversions. In our theoretical model, genotypes involve ordered combinations of DNA elements representing promoters, proteincoding genes, and transcription terminators; genotypic interconversions are driven by a recombinase enzyme that inverts DNA segments; and selectable phenotypes correspond to distinct patterns of gene expression. We analyze the microbial population as it evolves along a graph whose nodes are distinct genotypes and whose edges are interconversions. We show that the steady-state proportion of each genotype depends on its own growth advantage, as well as on its connectivity to other genotypes. Multiple phenotypes with identical or distinct growth rates can be indefinitely maintained in the population, while their proportion can be regulated by varying the rate of DNA flipping. Recombinase-based synthetic constructs have already been implemented; the graph-theoretic framework developed here will be useful in adapting them to generate microbial consortia.

The endoplasmic reticulum is permeable to a variety of small molecules, ranging from calcium to sugars and small peptides. We previously reported that constitutively-open, Sec61 translocons provide a non-selective pathway for small molecules to cross the ER membrane (Pflugers Arch., 457:917). The goal of the present study was to determine the size of the pathway through which small molecules passively cross the ER membrane by comparing the relative permeabilities of a series of neutral sugars, including ribose, galactose, sucrose, and raffinose. Rough ER microsomes from pig pancreas were immobilized on a coverslip, and a low-power, total internal reflection microscope was used to detect changes in light scattering produced when the flowing bath solution was changed from 140 mM K-Acetate/2.5 mM MgCl2/10 mM HEPES to the same solution supplemented with 100 mM of one of the sugars. All of the sugars produced an increase in scattering that recovered exponentially, with the rate of the recovery inversely proportional to the Stokes radius of the sugar. The time constants for recovery were fitted using a Bungay-Brenner function, which models a pore as a simple cylinder and permeation as diffusion without specific interaction of a permeant molecule with the wall of a pore. The relative permeabilities of the four sugars were fitted very well by the Bungay-Brenner function, yielding an average pore diameter of 15 angstroms. Thus, there appears to be a pathway for these sugars to cross the ER membrane that is constitutively active and can be modeled as a 15 angstrom pore. Furthermore, the release of nascent chains by puromycin increased the rate of recovery, whereas treatment with EDTA, which strips ribosomes from the ER membrane, decreased the rate of recovery. Both effects are consistent with the Sec61 translocon contributing to this pathway.